Hi all,
I just updated our development machine to the latest from galaxy-central, and it broke:
$ ./run.sh Traceback (most recent call last): File "/home/pjcock/repositories/galaxy-central/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/home/pjcock/repositories/galaxy-central/lib/galaxy/app.py", line 11, in <module> from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/home/pjcock/repositories/galaxy-central/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> from galaxy.web.base.controller import UsesHistory File "/home/pjcock/repositories/galaxy-central/lib/galaxy/web/base/controller.py", line 12, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/home/pjcock/repositories/galaxy-central/lib/galaxy/visualization/tracks/data_providers.py", line 16, in <module> from bx.arrays.array_tree import FileArrayTreeDict File "numpy.pxd", line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) ValueError: numpy.dtype does not appear to be the correct type object
I checked I had the latest numpy and bx_python egg files by removing them, Galaxy downloaded the same ones:
bx_python-0.7.0_494c2d1d68b3-py2.6-linux-x86_64-ucs2.egg numpy-1.6.0-py2.6-linux-x86_64-ucs2.egg
This is a 64 bit Linux machine. Any ideas what might be wrong? I'm guessing some Pyrex or Cython extension module in an egg file needs recompiling.
Note there is a system level install of NumPy 1.4.1 on this machine, but I believe the egg is used in preference?
Peter
On Thu, Jun 9, 2011 at 11:43 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
Hi all,
I just updated our development machine to the latest from galaxy-central, and it broke:
$ ./run.sh Traceback (most recent call last): File "/home/pjcock/repositories/galaxy-central/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/home/pjcock/repositories/galaxy-central/lib/galaxy/app.py", line 11, in <module> from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/home/pjcock/repositories/galaxy-central/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> from galaxy.web.base.controller import UsesHistory File "/home/pjcock/repositories/galaxy-central/lib/galaxy/web/base/controller.py", line 12, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/home/pjcock/repositories/galaxy-central/lib/galaxy/visualization/tracks/data_providers.py", line 16, in <module> from bx.arrays.array_tree import FileArrayTreeDict File "numpy.pxd", line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) ValueError: numpy.dtype does not appear to be the correct type object
I checked I had the latest numpy and bx_python egg files by removing them, Galaxy downloaded the same ones:
bx_python-0.7.0_494c2d1d68b3-py2.6-linux-x86_64-ucs2.egg numpy-1.6.0-py2.6-linux-x86_64-ucs2.egg
This is a 64 bit Linux machine. Any ideas what might be wrong? I'm guessing some Pyrex or Cython extension module in an egg file needs recompiling.
Note there is a system level install of NumPy 1.4.1 on this machine, but I believe the egg is used in preference?
Peter
It turned out to be quite quick to find what commit broke things:
hg checkout 6074:a6868407f0e8 --> fails
hg checkout 6073:d6b048e3483e --> works
Looks like 6074:a6868407f0e8 is the cause then, which makes sense since it jumps from NumPy 1.3.0 to NumPy 1.6.0:-
changeset: 6074:a6868407f0e8 user: Nate Coraor nate@bx.psu.edu date: Wed Jun 08 23:50:07 2011 -0400 summary: Testing Python 2.7.
https://bitbucket.org/galaxy/galaxy-central/changeset/a6868407f0e8
Probably some of the eggs need to be updated.
Peter
Peter Cock wrote:
It turned out to be quite quick to find what commit broke things:
hg checkout 6074:a6868407f0e8 --> fails
hg checkout 6073:d6b048e3483e --> works
Looks like 6074:a6868407f0e8 is the cause then, which makes sense since it jumps from NumPy 1.3.0 to NumPy 1.6.0:-
changeset: 6074:a6868407f0e8 user: Nate Coraor nate@bx.psu.edu date: Wed Jun 08 23:50:07 2011 -0400 summary: Testing Python 2.7.
https://bitbucket.org/galaxy/galaxy-central/changeset/a6868407f0e8
Probably some of the eggs need to be updated.
bx_python needs to be rebuilt using the new version of the numpy egg. I am doing this now and they should be up shortly.
--nate
Peter
Fixed on trunk.
On Thu, Jun 9, 2011 at 10:26 AM, Nate Coraor nate@bx.psu.edu wrote:
Peter Cock wrote:
It turned out to be quite quick to find what commit broke things:
hg checkout 6074:a6868407f0e8 --> fails
hg checkout 6073:d6b048e3483e --> works
Looks like 6074:a6868407f0e8 is the cause then, which makes sense since it jumps from NumPy 1.3.0 to NumPy 1.6.0:-
changeset: 6074:a6868407f0e8 user: Nate Coraor nate@bx.psu.edu date: Wed Jun 08 23:50:07 2011 -0400 summary: Testing Python 2.7.
https://bitbucket.org/galaxy/galaxy-central/changeset/a6868407f0e8
Probably some of the eggs need to be updated.
bx_python needs to be rebuilt using the new version of the numpy egg. I am doing this now and they should be up shortly.
--nate
Peter
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On Thu, Jun 9, 2011 at 4:25 PM, Kanwei Li kanwei@gmail.com wrote:
Fixed on trunk.
Confirmed, thank you.
Peter
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